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- PDB-8uwm: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8uwm
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound
ComponentsFluorophosphonate-binding serine hydrolase E
KeywordsHYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / borolane / covalent / boron-serine / boron-histidine
Function / homologyHydrolases / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / membrane / : / Uncharacterized hydrolase SAUSA300_2518
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: Nat Commun / Year: 2025
Title: Identification of covalent inhibitors of Staphylococcus aureus serine hydrolases important for virulence and biofilm formation.
Authors: Upadhyay, T. / Woods, E.C. / Dela Ahator, S. / Julin, K. / Faucher, F.F. / Uddin, M.J. / Hollander, M.J. / Pedowitz, N.J. / Abegg, D. / Hammond, I. / Eke, I.E. / Wang, S. / Chen, S. / ...Authors: Upadhyay, T. / Woods, E.C. / Dela Ahator, S. / Julin, K. / Faucher, F.F. / Uddin, M.J. / Hollander, M.J. / Pedowitz, N.J. / Abegg, D. / Hammond, I. / Eke, I.E. / Wang, S. / Chen, S. / Bennett, J.M. / Jo, J. / Lentz, C.S. / Adibekian, A. / Fellner, M. / Bogyo, M.
History
DepositionNov 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorophosphonate-binding serine hydrolase E
B: Fluorophosphonate-binding serine hydrolase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3058
Polymers62,5502
Non-polymers7556
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-117 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.887, 77.993, 110.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fluorophosphonate-binding serine hydrolase E


Mass: 31275.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: SAUSA300_2518 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-XPU / 2-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzene-1-sulfonamide


Mass: 297.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20BNO4S / Details: reacted form / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 13uL 19.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL Q41 (50mM in DMSO) and incubated at 18C overnight. 0.3 uL FphE-Q41 solution was mixed with 0.15 uL of reservoir ...Details: 13uL 19.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL Q41 (50mM in DMSO) and incubated at 18C overnight. 0.3 uL FphE-Q41 solution was mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180mM Calcium acetate, 100mM Tris pH 8.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% Ethylene glycol, 75% reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.97→45.8 Å / Num. obs: 41115 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Χ2: 1 / Net I/σ(I): 13.9 / Num. measured all: 329625
Reflection shellResolution: 1.97→2.02 Å / % possible obs: 98.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 1.093 / Num. measured all: 23058 / Num. unique obs: 2810 / CC1/2: 0.704 / Rpim(I) all: 0.401 / Rrim(I) all: 1.166 / Χ2: 1.03 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDS20220820data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→45.8 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 2064 5.03 %
Rwork0.1675 --
obs0.1695 41047 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 30 239 4655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124516
X-RAY DIFFRACTIONf_angle_d1.1956132
X-RAY DIFFRACTIONf_dihedral_angle_d7.215598
X-RAY DIFFRACTIONf_chiral_restr0.063664
X-RAY DIFFRACTIONf_plane_restr0.017804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.33871320.27682511X-RAY DIFFRACTION98
2.01-2.060.24311300.22792575X-RAY DIFFRACTION100
2.06-2.120.25091390.19662592X-RAY DIFFRACTION100
2.12-2.180.22281340.17752535X-RAY DIFFRACTION100
2.18-2.250.19581290.15682589X-RAY DIFFRACTION100
2.25-2.330.20531250.16562567X-RAY DIFFRACTION100
2.33-2.430.24111580.17132577X-RAY DIFFRACTION100
2.43-2.540.20531310.17842579X-RAY DIFFRACTION100
2.54-2.670.23381320.16152585X-RAY DIFFRACTION100
2.67-2.840.22741430.16972586X-RAY DIFFRACTION100
2.84-3.060.19341410.1712590X-RAY DIFFRACTION100
3.06-3.360.24661510.17872619X-RAY DIFFRACTION100
3.37-3.850.22281390.16022630X-RAY DIFFRACTION100
3.85-4.850.1551470.13492658X-RAY DIFFRACTION100
4.85-45.80.17461330.17582790X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.97990.2752-0.8612.8555-0.30752.70720.228-0.35340.48330.25090.0879-0.5558-0.48431.0466-0.27150.3875-0.1835-0.00260.6491-0.06730.434310.35520.1792-36.8636
21.69230.0266-0.28242.30560.32973.20760.1126-0.08220.3648-0.1492-0.0122-0.178-0.51920.4055-0.08370.3103-0.06690.02040.24660.01670.317-1.362619.9049-44.888
34.31550.6204-3.8151.1561-0.67483.3751-0.35920.1082-0.1906-0.0246-0.02270.0060.5895-0.30420.32590.3426-0.01760.0090.2509-0.0420.3209-17.03140.883-36.1083
41.17280.243-1.05490.0515-0.21180.96010.15870.06330.3176-0.1558-0.29770.29640.34120.24820.05740.57450.0078-0.03440.41410.00480.5003-33.86642.8316-21.3199
55.82934.36284.36958.3496.05534.8033-0.28050.353-0.0407-0.56850.22970.1676-0.13620.35970.12320.32820.0010.02090.31380.00690.3243-22.50519.3177-26.7045
63.114-0.4173-0.25652.0555-0.35762.4319-0.1146-0.44840.00820.38840.17250.1796-0.1649-0.164-0.060.33160.04190.02640.30730.01590.259-34.300215.9912-4.8709
71.3664-0.7099-0.36641.483-0.04431.82670.0045-0.04380.12140.06990.0452-0.0432-0.2364-0.0001-0.04910.2521-0.0129-0.0110.2138-0.00430.2458-26.412620.5976-16.5598
85.2205-2.9392-4.45994.4310.9734.6808-0.1174-0.28350.34310.6185-0.3551-0.64130.86480.64830.42210.65240.1167-0.00910.49840.06490.49234.2139-1.9309-33.8893
92.21210.0936-1.12051.49570.2483.4195-0.0624-0.0641-0.0037-0.0728-0.0336-0.28440.05370.7010.08010.26040.0108-0.00970.33450.02360.32143.40168.6199-47.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 183 )
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 200 )
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 166 )
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 276 )

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